fix(brain_extraction_wf): Pass inu_n4 to atropos_wf #2083
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ '**' ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: [ master, 'maint/*' ] | |
| schedule: | |
| - cron: '0 0 * * *' | |
| concurrency: | |
| group: python-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| check_if_skip: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_message: ${{ steps.get_commit_message.outputs.commit_message }} | |
| steps: | |
| - name: Get repo | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Print head git commit message | |
| id: get_commit_message | |
| run: | | |
| if [[ -z "$COMMIT_MSG" ]]; then | |
| COMMIT_MSG=$(git show -s --format=%s) | |
| fi | |
| echo commit_message=$COMMIT_MSG | tee -a $GITHUB_OUTPUT | |
| env: | |
| COMMIT_MSG: ${{ github.event.head_commit.message }} | |
| build: | |
| needs: check_if_skip | |
| if: "!contains(needs.check_if_skip.outputs.commit_message, '[skip ci]')" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3 | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Check python version and install build | |
| run: | | |
| python --version | |
| python -m pip install -U build twine | |
| - name: Build niworkflows | |
| run: python -m build | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| get_data: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Create test data directory | |
| run: mkdir -p $HOME/.cache/stanford-crn | |
| - name: Load test data cache | |
| uses: actions/cache@v3 | |
| id: stanford-crn | |
| with: | |
| path: ~/.cache/stanford-crn/ | |
| key: data-v0-${{ github.ref_name }}-${{ github.sha }} | |
| restore-keys: | | |
| data-v0-${{ github.ref_name }}- | |
| data-v0- | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: Verify environment | |
| run: | | |
| conda info | |
| which python | |
| - name: Install datalad | |
| run: | | |
| python -m pip install datalad-installer | |
| datalad-installer --sudo ok git-annex | |
| python -m pip install datalad datalad-osf | |
| datalad wtf | |
| - name: Pacify git | |
| run: | | |
| git config --global user.email "github@niworkflows.ci" | |
| git config --global user.name "Niworkflows Action" | |
| - name: Fetch test data | |
| run: | | |
| DS=$HOME/.cache/stanford-crn | |
| datalad install -r -s https://github.com/nipreps-data/niworkflows-data.git $DS | |
| cd $DS | |
| git -C BIDS-examples-1-enh-ds054 checkout enh/ds054 | |
| datalad update -r --merge -d . | |
| datalad get -J 2 -r ds000003 ds000030/sub-10228/func | |
| test: | |
| needs: [build, get_data] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, "3.10"] | |
| install: [repo] | |
| include: | |
| - python-version: "3.10" | |
| install: sdist | |
| - python-version: "3.10" | |
| install: wheel | |
| - python-version: "3.10" | |
| install: editable | |
| env: | |
| INSTALL_TYPE: ${{ matrix.install }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Load test data cache | |
| uses: actions/cache@v3 | |
| id: stanford-crn | |
| with: | |
| path: ~/.cache/stanford-crn/ | |
| key: data-v0-${{ github.ref_name }}-${{ github.sha }} | |
| - name: Load TemplateFlow cache | |
| uses: actions/cache@v3 | |
| id: templateflow | |
| with: | |
| path: ~/.cache/templateflow | |
| key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }} | |
| restore-keys: | | |
| templateflow-v0-${{ github.ref_name }}- | |
| templateflow-v0- | |
| - name: Fetch packages | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Select archive | |
| run: | | |
| if [ "$INSTALL_TYPE" = "sdist" ]; then | |
| ARCHIVE=$( ls dist/*.tar.gz ) | |
| elif [ "$INSTALL_TYPE" = "wheel" ]; then | |
| ARCHIVE=$( ls dist/*.whl ) | |
| elif [ "$INSTALL_TYPE" = "repo" ]; then | |
| ARCHIVE="." | |
| elif [ "$INSTALL_TYPE" = "editable" ]; then | |
| ARCHIVE="-e ." | |
| fi | |
| echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV | |
| - name: Install package | |
| run: python -m pip install $ARCHIVE | |
| - name: Check version | |
| run: | | |
| # Interpolate version | |
| if [[ "$GITHUB_REF" == refs/tags/* ]]; then | |
| TAG=${GITHUB_REF##*/} | |
| fi | |
| THISVERSION=$( python get_version.py ) | |
| THISVERSION=${TAG:-$THISVERSION} | |
| INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")') | |
| echo "VERSION: \"${THISVERSION}\"" | |
| echo "INSTALLED: \"${INSTALLED_VERSION}\"" | |
| test "${INSTALLED_VERSION}" = "${THISVERSION}" | |
| - name: Install test dependencies | |
| run: python -m pip install "niworkflows[tests]" | |
| - name: Set TEST_DATA_HOME | |
| run: echo "TEST_DATA_HOME=$HOME/.cache/stanford-crn" >> $GITHUB_ENV | |
| - name: Run tests | |
| run: pytest -sv --doctest-modules -n auto --cov niworkflows niworkflows | |
| - uses: codecov/codecov-action@v3 | |
| name: Submit to CodeCov | |
| test-pre: | |
| needs: [get_data, check_if_skip] | |
| if: ${{ !contains(needs.check_if_skip.outputs.commit_message, '[skip pre]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, "3.10"] | |
| install: [repo] | |
| pip-flags: ['--pre'] | |
| env: | |
| INSTALL_TYPE: ${{ matrix.install }} | |
| PIP_FLAGS: ${{ matrix.pip-flags }} | |
| steps: | |
| - name: Debug commit message | |
| run: echo "${{ needs.check_if_skip.outputs.commit_message }}" | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Load test data cache | |
| uses: actions/cache@v3 | |
| id: stanford-crn | |
| with: | |
| path: ~/.cache/stanford-crn/ | |
| key: data-v0-${{ github.ref_name }}-${{ github.sha }} | |
| - name: Load TemplateFlow cache | |
| uses: actions/cache@v3 | |
| id: templateflow | |
| with: | |
| path: ~/.cache/templateflow | |
| key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }} | |
| restore-keys: | | |
| templateflow-v0-${{ github.ref_name }}- | |
| templateflow-v0- | |
| - name: Install package | |
| run: python -m pip install $PIP_FLAGS . | |
| - name: Check version | |
| run: | | |
| # Interpolate version | |
| if [[ "$GITHUB_REF" == refs/tags/* ]]; then | |
| TAG=${GITHUB_REF##*/} | |
| fi | |
| THISVERSION=$( python get_version.py ) | |
| THISVERSION=${TAG:-$THISVERSION} | |
| INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")') | |
| echo "VERSION: \"${THISVERSION}\"" | |
| echo "INSTALLED: \"${INSTALLED_VERSION}\"" | |
| test "${INSTALLED_VERSION}" = "${THISVERSION}" | |
| - name: Install test dependencies | |
| run: python -m pip install $PIP_FLAGS "niworkflows[tests]" | |
| - name: Set TEST_DATA_HOME | |
| run: echo "TEST_DATA_HOME=$HOME/.cache/stanford-crn" >> $GITHUB_ENV | |
| - name: Run tests | |
| run: pytest -sv --doctest-modules -n auto --cov niworkflows niworkflows | |
| - uses: codecov/codecov-action@v3 | |
| name: Submit to CodeCov | |
| flake8: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.7 | |
| - run: pip install flake8 | |
| - run: flake8 niworkflows/ |